It’s a big day for Aileron Therapeutics. The Cambridge, MA-based biotech firm announced this morning it has formed a partnership with Swiss drug and diagnostics giant Roche to discover, develop, and commercialize a new class of drugs known as “stapled peptides.”

Under the terms of the deal, Roche (OTCQX: RHHBY) will provide at least $25 million in technology access fees and R&D support to Aileron. What’s more, Aileron will be eligible to receive up to $1.1 billion in milestone payments if drug candidates are developed against five targets from Roche’s main therapeutic areas—oncology, virology, inflammation, metabolism, and the central nervous system. Aileron will also receive royalties on future sales for any marketed products resulting from the collaboration.

This is Aileron’s first major industry collaboration—and a big step forward for the company. My colleague Luke first wrote about Aileron back in November 2008, when the startup talked about its plan to develop peptide-based drug compounds that block interactions between proteins in the body that can’t be affected by conventional small-molecule chemical drugs or genetically engineered protein drugs. The peptides apparently work because they’ve been chemically “stapled” to resist unraveling under the influence of enzymes in the body that would render them useless.

Last year, Aileron closed a $40 million financing round led by the venture arm of GlaxoSmithKline and Boston-based Excel Medical Ventures, with participation from Novartis, Eli Lilly, Apple Tree Partners, and, yes, Roche. Aileron was founded in 2005 by the late Stanley Korsmeyer and Loren Walensky, a pair of biologists from Harvard Medical School and the Dana-Farber Cancer Institute, and Gregory Verdine, a Harvard University chemist.

It’s still very early for the company, in terms of any possible clinical impact. But last November, scientists at Harvard, Dana-Farber, and the Broad Institute of Harvard and MIT reported promising results from multiple disease models and animal tests, when they used a stapled peptide from Aileron to stop the production of a protein associated with uncontrolled growth of cancer cells. The hope is that stapled peptide drugs might be able to target previously “undruggable” protein targets inside cells, without the side effects of existing drugs.

In any case, the deal with one of the world’s biggest biotechs seems to support Aileron’s approach to date. “This alliance with Roche validates the broad potential for our Stapled Peptide platform across multiple therapeutic areas and classes of targets and also provides Aileron with capital to advance our platform and internal drug development pipeline” said Joe Yanchik, Aileron’s president and CEO, in a statement.

Gregory T. Huang is Xconomy's Deputy Editor, National IT Editor, and Editor of Xconomy Boston. E-mail him at gthuang [at] xconomy.com. Follow @gthuang